Chapter 15

Part I: Gene RegulationPart II: Mutations

Part I: Gene Regulation

Prokaryotic Gene Regulation

• Simpler organisms: simpler system. Easier to study.

• “Operon”: A region of the prokaryotic genome that encodes for several polypeptides all involved in a single metabolic pathway

A C D

E1 E2 E3

B

Concepts• Repressible

– Example: trp operon.– Encodes enzymes to synthesize the amino acid tryptophan. Usually

this operon is “on”. However, if there is a lot of tryptophan, the operon will turn “off”.

• Generally associated with anabolic pathways (building stuff that isn’t there)

• Inducible– Example: lac operon– Encodes enyzmes that break down lactose into usable molecules (like

glucose)– Usually off (the cell prefers glucose, not lactose). When there is little

glucose, the cell turns this on so it can use an alternative energy supply.

• Generally associated with catabolic pathways (breaking stuff down)

Prokaryotic Gene Regulation

• E1, E2, E3, are all encoded along a single stretch of DNA, and all controlled by a single promoter region.

• Movie: the lac operon

E1 E2 E3Promoter Operator

Additional Control

• To “fine tune” gene expression, all genes are controlled in more than one way (it’s not as simple as a repressor protein binding to an operator).

• Example: in addition to the concentration of lactose (which causes the repressor to fall off, remember), the concentration of glucose also helps control gene expression.

Additional Control

• High glucose– Low cAMP

• Low glucose– High cAMP– Binds to “CAP” (catabolite activating protein)– CAP/cAMP binds to CAP binding site next to the promoter.– Causes DNA to bend, favoring attachement of RNA polymerase

• High lactose– Repressor falls off, activating the lac operon

• Low lactose– Repressor stays attached to operator, preventing transcription

Eukaryotic Gene Expression

• Chromatin Structure– Histones, epigenetic inheritance, heterochromatin,

euchromatin• Transcriptional Control– Transcription factors– transposons

• Post-Transcriptional Control• Translational Control• Post-Translational Control

Part II: Mutations

Mutation Definition• Used to be something that causes a change in phenotype.• Now we know it’s a change in the DNA sequence of a gene.

Mutations

Point Mutations

MisssenseSilent

Nonsense

RadicalConservative

A change in the 3rd base position of a codon. The

protein sequence does not change.

A mutation in a codon that changes the encoded amino

acid.

The new amino acid has strikingly different

biochemical properties than the original

The new amino acid has similar biochemical

properties as the original

A codon that normally encodes an amino acid is

mutated to encode a “STOP” signal

Frameshift

A single base is inserted or deleted, resulting in the codons being read in a

different reading frame.

THE CAT ATE THE RAT

THE ATA TET HER AT

5’-UCUUAUUGUAGA-3’

5’-UCUUAUUGUAGA-3’

5’-UCAUAUUGUAGA-3’

Silent Mutation

UCU UCASer Ser

Silent because the protein hasn’t changed at all.

5’-UCUUAUUGUAGA-3’

5’-UCUUAUUGUAGA-3’

5’-ACUUAUUGUAGA-3’

Missense Mutation

UCU ACUSer Thr

Conservative, because Ser and Thr are similar.

Ser and Thr differ by a single methyl group.

UCUUCCUCAUCG

They also differ by a single base in their codons…

SER THR

ACUACCACAACG

(ACU)(ACC)

AGUAGC

5’-UCUUAUUGUAGA-3’

5’-UCUUAUUGUAGA-3’

5’-UGUUAUUGUAGA-3’

Missense Mutation

UCU UGUSer Cys

Radical, because Ser and Cys are very different biochemically

5’-UCUUAUUGUAGA-3’

5’-UCUUAUUGUAGA-3’

5’-UGUUAUUGUAGA-3’

Missense Mutation

UCU UGUSer Cys

Radical, because Ser and Cys are very different biochemically

5’-UCUUAUUGUAGA-3’

5’-UCUUAUUGUAGA-3’

5’-UCUUAUUGUUGA-3’

Nonsense Mutation

AGA UGAArg “STOP”

Nonsense because No additional translation occurs.

5’-UCUUAUUGUUGA-3’

Nonsense Mutation

Proteins resulting from a nonsense mutation are said to be “truncated” (same definition used in math)

truncatedFull Length

Mutations

Effects– Protein function (remember hemoglobin)– Gene Regulation

• E.g. Mutate promoter region that affects RNA Polymerase binding.

– Germ Cell Mutations (Evolutionarily Important)• Mutations that occur in eggs and sperm.

– Somatic Cell Mutations• Somatic cells are body cells – the normal, diploid cells that are not involved in

sexual reproduction. These mutations are NOT inherited.

– Aging effects• Mitochondrial mutation leads to aging• Not necessarily… (good article)

5’-UCUGAGUGUAGA-3’

5’-UCUGUGUGUAGA-3’

Protein Function

5’-ACGTACTATAGCAGCATGGATCGAATCGATACACT-3’

3’-TGCATGATATCGTCGTACCTAGCTTAGCTATGTGA-5’

(how you used to see it before this class)

5’-ACGTACTATAGCAGCATGGATCGAATCGATACACT-3’

How you should see it now.

TATA Box is a promoter sequence that the protein TBP binds.TBP (TATA Binding Protein) recruits RNA Polymerase to the promoter to turn it “on”.

Notice the start site.

If “TATA” gets mutated, TBP can’t bind. RNA Polymerase is no longer recruited.The gene is shut down.

Gene Regulation

Mutations

Causes– DNA replication errors

• Prokaryotes have high error rates; eukaryotes have very low (1 in a billion). But they DO happen.

Mutations

Causes– Radiation

• Energy from subatomic particles is absorbed by organic molecules.• This causes bonds to break.• The high energy biproducts form new bonds.• These new bonds are abnormal.• If this happens within DNA, it leads to changes in the genetic code.

DNA Damage To Nuclear Test Vets Prompts Call For Study Of Children (5/16/2007)

Mutations

Causes– Chemicals

• From the National Cancer Institute• Cigarette smoke contains about 4,000 chemical agents, including over

60 carcinogens (8). In addition, many of these substances, such as carbon monoxide, tar, arsenic, and lead, are poisonous and toxic to the human body. Nicotine is a drug that is naturally present in the tobacco plant and is primarily responsible for a person’s addiction to tobacco products, including cigarettes. During smoking, nicotine is absorbed quickly into the bloodstream and travels to the brain in a matter of seconds. Nicotine causes addiction to cigarettes and other tobacco products that is similar to the addiction produced by using heroin and cocaine (9).

• Nicotine itself inhibits apoptosis.

Kinds of DNA Damage

double strand DNA damage

Single strand DNA damage

Like a watch wrapped around a wrist, a special enzyme encircles the DNA double helix. Using a combination of imaging techniques, researchers have captured snapshots of the enzyme, DNA ligase, joining together a broken strand of DNA. Millions of DNA breaks occur during the normal course of a cell's life. Without molecules that can connect the pieces, cells can malfunction, die, or become cancerous. Courtesy of Tom Ellenberger, Washington University School of Medicine in St. Louis

MutationsRepair– Role of DNA polymerase

• 3'->5' exonuclease activity• One example: (from same ref as below): Oxidation of G to form oxoG

produces a subtle structural transformation – This results in deleterious mutations because DNA polymerases misread

oxoG as a thymine (T) base during replication.

– repair enzymes (ref)• DNA-repair enzymes have the ability to search through vast tracts of

DNA to find subtle anomalies in the structure • The information content of the DNA double helix is preserved by a crew

of DNA-repair enzymes that defend the genome from the harmful effects of DNA damage

Note the difference between

chromosomal mutations gene mutations

Quick!– Lampbrush chromosomes– Polytene chromosomes

Polytene Chromosomes

Polytene chromosomes form when multiple rounds of replication produce chromatids that remain synapsed together in a haploid number of chromosomes